Testing the Waters: Diversification and Selection in the \u3cem\u3eNerodia fasciata/clarkii\u3c/em\u3e Species Complex

Understanding evolution is a key component in trying to decipher the processes generating global species diversity. The strength, direction, and interaction of gene flow and selection often determine diversification patterns and the process of speciation. The Nerodia fasciata/clarkii species complex, a lineage of water snakes, is thought to have high levels of both gene flow and selective pressures due to ecological constraint. Nerodia clarkii resides in salt marsh and estuarine habitats while Nerodia fasciata is typically found in fresh water. Salinity is a strong selective pressure and is thought to play a role in the diversification process. Currently, there are five described subspecies within the complex but their validity is in question, causing concerns about the conservation status of the federally threatened Atlantic Salt Marsh Snake (N. c. taeniata). To understand the diversification of the Nerodia fasciata/clarkii complex and to resolve the noted taxonomic issues, I generated the first population genomic dataset for this group using double digest restriction site-associated DNA sequencing (ddRADseq). I first used a Discriminate Analysis of Principal Components (DAPC) to identify population structure and SVDQuartets to generate a coalescent based phylogeny. With these data, I identified 4-6 populations that approximate subspecies designations although only one assigned subspecies, N. c. clarkii, was monophyletic. Second, I estimated migration among the best supported population clustering (k=5) using Estimated Effective Migration Surfaces (EEMS). EEMS revealed a migration corridor between the mostly N. fasciata populations and a reduction in gene flow at the coasts. Third, I used two selection scan analyses and one environmental association analysis to identify genes that are putatively under selection with an emphasis on local adaptation to saline water. I found 10 candidate genes that may be involved in osmoregulation and multiple correlations to temperature and precipitation. My results indicate that the two species are valid, and that four subspecies are also evolutionary lineages. Although gene flow and population assignment tests provided evidence that N. c. taeniata was isolated from other populations I could not unambiguously determine its validity. Both the candidate gene frequencies and EEMS indicate that majority N. fasciata populations mostly share a selection regime and gene flow patterns separate them from N. clarkii. This may demonstrate how a reduction in gene flow and a change in selection pressures can generate species diversity

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow

Cancer-Related Symptom Clusters, Eosinophils, and Survival in Hepatobiliary Cancer: An Exploratory Study

CONTEXT: The study of symptom clusters is gaining increased attention in the field of oncology in an attempt to improve the quality of life of patients diagnosed with cancer. OBJECTIVES: The aims of the present study were to: (1) determine the prevalence and distribution of pain, fatigue, and symptoms of depression and their covariation as a cluster in people with hepatobiliary carcinoma; (2) characterize how variation in each individual symptom and/or their covariation as a cluster are associated with changes in immunity; and (3) determine if the symptom clusters, and associated biomarkers, are related to survival in people diagnosed with hepatobiliary carcinoma. METHODS: Two hundred and six participants diagnosed with hepatobiliary carcinoma completed a battery of standardized questionnaire measuring cancer-related symptoms. Peripheral blood leukocytes were measured at diagnosis, three- and six-month follow-ups. Survival was measured from the date of diagnosis to death. RESULTS: Cancer-related symptoms were prevalent and two-step hierarchical cluster analyses yielded three clusters. High levels of pain, fatigue, and depression were found to be associated with elevated eosinophil percentages (F[1,78]=3.1, P=0.05) at three-month and six-month follow-ups using repeated measures ANOVA. Using multivariate latent growth curve modeling, pain was the primary symptom associated with elevated eosinophil percentages between diagnosis and six months (z=2.24, P=0.05). Using Cox regression, vascular invasion and age were negatively associated with survival (Chi-square=21.6, P=0.03). While stratifying for vascular invasion, Kaplan Meier survival analysis was performed and eosinophil levels above the median for the sample were found to be related to increased survival in patients with and without vascular invasion (Breslow Chi-square=4.9, P=0.03). Symptom clusters did not mediate the relationship between eosinophils and survival. CONCLUSION: Cancer-related symptoms, particularly pain and depression, were associated with increased percentages of eosinophils. The presence of symptoms may reflect tumor cell death and be indicative of response to treatment, or other processes, in patients with hepatobiliary carcinoma